Video Sequence Editor: change all data/files paths with python
There are many great VSE add ons that you could look at for inspiration. Also consider reducing your complexity. Perhaps you could create sub scenes, each containing the png sequence you need. then you could iterate those scene strips in your master VSE scene.

After setting up a repetition of the strip stacks (in the master scene) you could make a simple command line render of the master scene with an array for start / end frames to give you discreet composited renders.